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I'm building up an Madone 7 for a friend and installing an FC-9000 (Dura-Ace) crank in the BB90 bottom bracket. With the bearings fully seated, it appears that the leftside arm does not slide onto the crank axle quite as far as I have experienced on other bikes I have built in the past.

Researching BB standards, the BB90 appears to be the widest at 90.5mm for road.

Thus on a related note, Shimano also sells two (2) different crank fixing bolts. (Version 1 and Version 2). The difference is thread length. Version 1 thread length is approx 8.5mm and version 2 is approx 16mm. I am assuming the version 2 is for these situations where the slightly wider bottom bracket causes the crank arm to engage on the splines slightly less.

Waiting on the crank fixing bolt to arrive (ver 2), but asking for input to see if I'm interpreting this correctly. Engagement of the arm on the splines seems to be about half, although that appears to be per design?

The crank fixing bolt is not designed to lock the crank arm in place. It's only used to apply the right amount of 'pre-load' on the bearings. The two smaller bolts in the crank arm fixate the crank arm on the axle.

So, basically, if the thread on your version 1 bolt engages, you should be fine. Just give the crank a tap like crimsonbadger says.